6-32476421-G-T

Variant names:

• chr6-32476421-G-T
• rs12194148
• ENST00000829864.1:n.273+2212G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000829864.1(ENSG00000307923):​n.273+2212G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,720 control chromosomes in the GnomAD database, including 11,670 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11670 hom., cov: 43)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 29 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307923	ENST00000829864.1	n.273+2212G>T		intron_variant	Intron 2 of 2
ENSG00000307923	ENST00000829865.1	n.269+2212G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57789 AN: 151602 Hom.: 11663 Cov.: 43

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.381 AC: 57827 AN: 151720 Hom.: 11670 Cov.: 43 AF XY: 0.381 AC XY: 28255 AN XY: 74162

African (AFR) AF: 0.273 AC: 11305 AN: 41370

American (AMR) AF: 0.432 AC: 6570 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1650 AN: 3462

East Asian (EAS) AF: 0.377 AC: 1950 AN: 5170

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4814

European-Finnish (FIN) AF: 0.442 AC: 4662 AN: 10546

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28563 AN: 67830

Other (OTH) AF: 0.388 AC: 818 AN: 2106

Alfa AF: 0.320 Hom.: 1975

Asia WGS AF: 0.326 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12194148; hg19: chr6-32444198;